IMP Namespace Reference

Detailed Description

The IMP kernel provides base classes and key shared functionality.

Author:: Daniel Russel, Ben Webb

Version:: 1.0

Overview:: The IMP kernel provides the base functionality and abstract base classes for representation, scoring and sampling. In addition it provides basic functionality such as I/O, logging and Error Reporting support as well as tools to help implement functionality.

Examples: Examples can be found on the IMP.kernel examples page.

License:: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

Daniel Russel, Keren Lasker, Ben Webb, Dina Schneidman, Javier Velazquez-Muriel, Andrej Sali, “Integrative assembly modeling using IMP”, submitted, 2010. This paper provides an overview of the key concepts in IMP and how to apply them to biological problems.
Frank Alber, Friedrich Foerster, Dmitry Korkin, Maya Topf, Andrej Sali, “Integrating diverse data for structure determination of macromolecular assemblies”, Annual Review of Biochemistry, 2008. This paper provides a review of the integrative structure determination methodology and various data sources that can be used.


Namespaces
namespace	algebra
	This module contains general purpose algebraic and geometric methods.
namespace	atom
	This module contains functionality for dealing with atoms and proteins.
namespace	benchmark
	This module provides benchmarks of a variety of aspects of `IMP`.
namespace	container
	This module provides containers in `IMP`.
namespace	core
	This module contains basic functionality that is expected to be used by a wide variety of `IMP` users.
namespace	display
	This module provides support for displaying and exporting `IMP` data in various ways.
namespace	domino
	This module provides a framework for applying a divide-and-conquer sampling.
namespace	em
	This module allows density maps to be used to generate restraints.
namespace	example
	This module provides example showing how to implement various types of objects and functionality in `IMP`.
namespace	gsl
	This module wraps optimizers from the GNU Scientific Library.
namespace	helper
	This module provides high level functionality to assist in setting up and manipulating models.
namespace	misc
	This module contains miscellaneous and experimental functionality.
namespace	modeller
	This module contains functionality for integrating Modeller with IMP.
namespace	restrainer
	This module provides a higher level interface for using experimental proteomics data with `IMP`.
namespace	saxs
	This module adds small angle x-ray scatter support to `IMP`.
namespace	statistics
	This module provides methods for clustering.
namespace	test
	Methods and classes for testing the IMP kernel and modules.
Data Structures
class	ConfigurationSet
	A class to store a set of configurations of a model. More...
class	Constraint
	Implement a constraint on the Model. More...
class	Container
	Abstract class for containers of particles. More...
class	Containers
class	ContainersTemp
class	Decorator
class	DerivativeAccumulator
	Class for adding derivatives from restraints to the model. More...
class	DumpModelOnFailure
	Dump the state of the model to a file on an error and then go on the the other handlers. More...
class	Exception
	The general base class for `IMP` exceptions. More...
class	FailureHandler
class	FailureHandlerBase
	A base class for setting up failure handlers. More...
class	FloatKey
	The type used to identify float attributes in the Particles. More...
class	IncreaseIndent
	Increase the current indent in the log by one level. More...
class	IndexException
	An exception for a request for an invalid member of a container. More...
struct	InternalException
	A general exception for an intenal error in IMP. More...
class	IntKey
	The type used to identify int attributes in the Particles. More...
class	IOException
	An input/output exception. More...
class	KeyBase
	A base class for Keys. More...
class	Model
	Class for storing model, its restraints, constraints, and particles. More...
class	ModelException
	An exception which is thrown when the Model has attributes with invalid values. More...
class	Object
	Common base class for heavy weight `IMP` objects. More...
class	ObjectKey
	The type used to identify a particle attribute in the Particles. More...
class	Optimizer
	Base class for all optimizers. More...
class	OptimizerState
	Shared optimizer state. More...
class	OptimizerStates
class	OptimizerStatesTemp
class	PairContainer
	A shared container for particle_pairs. More...
class	PairContainers
class	PairContainersTemp
	A collection of containers. More...
class	PairFilter
	A shared filter for particle_pairs. More...
class	PairFunctor
	Create a functor which can be used with build in C++ and python commands. More...
class	PairModifier
	A base class for modifiers of ParticlePairs. More...
class	PairScore
	Abstract score function. More...
class	PairScores
class	PairScoresTemp
class	Particle
	Class to handle individual model particles. More...
class	ParticleKey
	The type used to identify a particle attribute in the Particles. More...
class	Particles
class	ParticlesTemp
class	ParticleTuple
	A class to store a tuple of particles. More...
class	Pointer
	A reference counted pointer to an object. More...
class	QuadContainer
	A shared container for particle_quads. More...
class	QuadContainers
class	QuadContainersTemp
	A collection of containers. More...
class	QuadFilter
	A shared filter for particle_quads. More...
class	QuadFunctor
	Create a functor which can be used with build in C++ and python commands. More...
class	QuadModifier
	A base class for modifiers of ParticleQuads. More...
class	QuadScore
	Abstract score function. More...
class	QuadScores
class	QuadScoresTemp
class	RAII
	RAII-style objects. More...
class	RefCounted
	Common base class for ref counted objects. More...
class	Refiner
	Abstract class to implement hierarchical methods. More...
class	Restraint
	Abstract class for representing restraints. More...
class	Restraints
class	RestraintSet
	Container used to hold a set of restraints. More...
class	RestraintsTemp
class	Sampler
	Base class for all samplers. More...
class	SaveOptimizeds
	Save and restore the set of optimized attributes for a set of particles. More...
class	ScopedFailureHandler
	Control a scope-dependent failure handler. More...
class	ScoreState
	Shared score state. More...
class	ScoreStatePointer
	Removes the ScoreState when the RAII object is destroyed. More...
class	ScoreStates
class	ScoreStatesTemp
class	SetLogState
	A class to change and restore log state. More...
class	SetLogTarget
class	SingletonContainer
	A shared container for particles. More...
class	SingletonContainers
class	SingletonContainersTemp
	A collection of containers. More...
class	SingletonFilter
	A shared filter for particles. More...
class	SingletonFunctor
	Create a functor which can be used with build in C++ and python commands. More...
class	SingletonModifier
	A base class for modifiers of Particles. More...
class	SingletonScore
	Abstract score function. More...
class	SingletonScores
class	SingletonScoresTemp
class	StringKey
	The type used to identify string attributes in the Particles. More...
class	TextInput
class	TextOutput
class	TripletContainer
	A shared container for particle_triplets. More...
class	TripletContainers
class	TripletContainersTemp
	A collection of containers. More...
class	TripletFilter
	A shared filter for particle_triplets. More...
class	TripletFunctor
	Create a functor which can be used with build in C++ and python commands. More...
class	TripletModifier
	A base class for modifiers of ParticleTriplets. More...
class	TripletScore
	Abstract score function. More...
class	TripletScores
class	TripletScoresTemp
class	UnaryFunction
	Abstract single variable functor class for score functions. More...
class	UsageException
	An exception for an invalid usage of `IMP`. More...
class	ValueException
	An exception for an invalid value being passed to `IMP`. More...
class	VectorOfRefCounted
	A vector-like container for reference counted objects. More...
class	VersionInfo
	Version and module information for Objects. More...
class	WeakPointer
	A weak pointer to an IMP::Object or IMP::RefCountedObject. More...
Error checking and reporting
By default `IMP` performs a variety of runtime error checks. These can be controlled using the IMP::set_check_level function. Call IMP::set_check_level with IMP::NONE to disable all checks when you are performing your optimization as opposed to testing your code. Make sure you run your code with the level set to at least USAGE before running your final optimization to make sure that `IMP` is used correctly. Error handling is provided by IMP/exception.h, Use the `gdbinit` file provided in `tools` to automatically have `gdb` break when `IMP` errors are detected.
enum	CheckLevel { NONE = 0, USAGE = 1, USAGE_AND_INTERNAL = 2 }
	Determine the level of runtime checks performed. More...
CheckLevel	get_check_level ()
	Get the current audit mode.
CheckLevel	get_maximum_check_level ()
	Determine the maximum check level that can be used for this build.
void	set_check_level (CheckLevel tf)
	Control runtime checks in the code.
void	set_print_exceptions (bool tf)
	Set whether exception messages are printed or not.
Logging
`IMP` provides tools for controlling the amount of log output produced and directing it to the terminal or a file. Only log messages tagged with a lower level than the current LogLevel are emitted. In addition to a global log level (get_log_level(), set_log_level()), each IMP::Object has an internal log level (IMP::Object::get_log_level(), IMP::Object::set_log_level()) which is used when executing code on that object. Logging is provided by IMP/log.h. People implementing IMP::Object classes should also see IMP_OBJECT_LOG() and IMP::SetLogState. All logging is disabled when `IMP` is built using `build='fast'`.
enum	LogLevel { DEFAULT = -1, SILENT = 0, WARNING = 1, TERSE = 2, VERBOSE = 3, MEMORY = 4 }
	The log levels supported by `IMP`. More...
void	add_to_log (std::string to_write)
	Write a string to the log.
LogLevel	get_log_level ()
	Get the currently active log level.
void	set_log_level (LogLevel l)
	Set the current global log level.
Typedefs
typedef std::pair< double, double >	DerivativePair
	A pair representing a function value with its first derivative.
typedef double	Float
	Basic floating-point value (could be float, double...).
typedef std::pair< Float, Float >	FloatRange
	A pair representing the allowed range for a Float attribute.
typedef std::vector< Float >	Floats
	Standard way to pass a bunch of Float values.
typedef int	Int
	Basic integer value.
typedef std::pair< Int, Int >	IntRange
typedef std::vector< IntRange >	IntRanges
typedef std::vector< Int >	Ints
	Standard way to pass a bunch of Int values.
typedef VectorOfRefCounted < Object * >	Objects
	A class which is used for representing collections of Object objects.
typedef std::vector< Object * >	ObjectsTemp
	A type to use when returning sets of objects so as to avoid refcounting.
typedef ParticleTuple< 2 >	ParticlePair
typedef VectorOfRefCounted < ParticleTuple < 2 >, RefCountParticleTuple< 2 > >	ParticlePairs
typedef std::vector < ParticleTuple< 2 > >	ParticlePairsTemp
typedef ParticleTuple< 4 >	ParticleQuad
typedef VectorOfRefCounted < ParticleTuple < 4 >, RefCountParticleTuple< 4 > >	ParticleQuads
typedef std::vector < ParticleTuple< 4 > >	ParticleQuadsTemp
typedef std::vector < ParticlesTemp >	ParticlesList
typedef ParticleTuple< 3 >	ParticleTriplet
typedef VectorOfRefCounted < ParticleTuple < 3 >, RefCountParticleTuple< 3 > >	ParticleTriplets
typedef std::vector < ParticleTuple< 3 > >	ParticleTripletsTemp
typedef ::boost::rand48	RandomNumberGenerator
typedef VectorOfRefCounted < Refiner * >	Refiners
	a collection of Refiner objects
typedef std::string	String
	Basic string value.
typedef std::vector< String >	Strings
	Standard way to pass a bunch of String values.
Attribute Keys
Each type of attribute has an associated type of key. The keys can be constructed from a string. Such construction can be expensive and so the resulting keys should be cached.
typedef std::vector< FloatKey >	FloatKeys
typedef std::vector< IntKey >	IntKeys
typedef std::vector< ObjectKey >	ObjectKeys
typedef std::vector< ParticleKey >	ParticleKeys
typedef std::vector< StringKey >	StringKeys
Functions
void	add_failure_handler (FailureHandler *f)
	Add a custom function to be called on an error.
	BOOST_STATIC_ASSERT (0 &&"The boost version IMP is built with must match the current one.")
std::string	get_data_path (std::string file_name)
	Return the path to installed data for this module.
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module.
TextOutput	get_log_target ()
std::string	get_module_name ()
const VersionInfo &	get_module_version_info ()
template<class O , class I >
O *	object_cast (I *o)
void	remove_failure_handler (FailureHandler *f)
	Remove a failure handler from the list.
void	set_log_target (TextOutput l)
	Set the target for the log.
void	set_print_deprecation_messages (bool tf)
	Toggle printing of warnings on using deprecated classes.
Model IO
Models can be written to files in an easy-to-read file format based on “name: value” pairs on separate lines with indentation used to indicated nesting (as in Python). The functions take a list of the particles to write/read. The particles need to be provided in the same order for reading and writing. This is not checked. If a passed particle has a particle attribute which is a particle not in the list, an IOException is thrown. This can change to silently ignoring such attributes if desired. Note: If you are just interested in saving the state of a model during runtime, use an IMP::ConfigurationSet instead. It should be substantially faster.
void	read_model (TextInput in, const ParticlesTemp &particles, Model *m)
void	write_model (Model *m, const ParticlesTemp &particles, TextOutput out)
Variables
static const double	PI = 3.1415926535897931
	the constant pi
RandomNumberGenerator	random_number_generator
	A shared random number generator.

Typedef Documentation

typedef std::vector<Object*> IMP::ObjectsTemp

A type to use when returning sets of objects so as to avoid refcounting.

Always store using Objects instead, but return ObjectsTemp. Objects can be constructed from a ObjectsTemp and vice versa.

Enumeration Type Documentation

enum IMP::CheckLevel

Determine the level of runtime checks performed.

NONE means that minimial checks are used.
- USAGE means that checks of input values to functions and classes are verified.
- USAGE_AND_INTERNAL adds checks that IMP itself is correct. Turn these on if you suspect an IMP bug or are developing Restraints or other IMP classes.

enum IMP::LogLevel

The log levels supported by IMP.

DEFAULT is only local logging (like in IMP::Object); it means to use the global log level.

VERBOSE prints very large amounts of information. It should be enough to allow the computational flow to be understood.

TERSE prints a few lines per restraint or per state each time the score is evaluated.

WARNING prints only warnings.

MEMORY prints information about allocations and deallocations to debug memory issues.

Function Documentation

std::string IMP::get_data_path ( std::string file_name )

Return the path to installed data for this module.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

    std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

std::string IMP::get_example_path ( std::string file_name )

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

    IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb", model));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

LogLevel IMP::get_log_level ( )

Get the currently active log level.

This may not always match the value passed to set_log_level() as objects can temporarily override the global level while they are evaluating.

CheckLevel IMP::get_maximum_check_level ( )

Determine the maximum check level that can be used for this build.

For example, 'fast' builds can't use any checks.

template<class O , class I >

O* IMP::object_cast ( I * o )

Up (or down) cast an IMP Object-derived class. If the cast does not succeed a ValueException will be thrown. Use a dynamic_cast if you prefer to have a NULL returned.

void IMP::set_check_level ( CheckLevel tf )

Control runtime checks in the code.

The default level of checks is USAGE for release builds and USAGE_AND_INTERNAL for debug builds.

void IMP::set_log_level ( LogLevel l )

Set the current global log level.

Note that this should not, currently, be used directly during Model::evaluate() calls.

void IMP::set_log_target ( TextOutput l )

Set the target for the log.

See TextOutput for options. Python users should use SetLogTarget instead.

void IMP::set_print_deprecation_messages ( bool tf )

Toggle printing of warnings on using deprecated classes.

If set to true (the default) a warning is printed every time a class marked as deprecated is used.

See also:: IMP_DEPRECATED

void IMP::set_print_exceptions ( bool tf )

Set whether exception messages are printed or not.

By default the error message associated with thrown exceptions are printed when using from C++, but not from Python (since the error messages of an unhandled exception are printed by the Python runtime).

Variable Documentation

RandomNumberGenerator IMP::random_number_generator

A shared random number generator.

The random number generator is seeded based of of the current time. To provide a better seed or use a constant seed call random_number_generator.seed(x) with a 32 bit int or a 64 bit unsigned int.

This generator can be used by the Boost.Random distributions.

IMP Namespace Reference

Detailed Description

Namespaces

Data Structures

Error checking and reporting

Logging

Typedefs

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation